Protein nanofibers (PNFs) created by controlling the self-assembly of protein molecules are contemporary biomacromolecular precursors to construct novel functional nanomaterials. We report here on a facile approach to prepare PNF-based biophotonic nanohybrids. For the first time we demonstrate the creation of fibronectin (FN) nanofibers in highly concentrated ethanol solution and subsequently present the organization of N-hydroxysulfosuccinimide (NHS) modified CdSe–ZnS core–shell quantum dots (QDs) on the self-assembled FN nanofibers by covalent interaction. AFM and TEM results indicate that the formation of FN nanofibers is controllable and the created FN nanofibers are uniform in diameter and length. UV-vis and XPS data identified the successful modification of QDs. The one-dimensional (1-D) PNF–QD biophotonic nanohybrids created by organizing QDs onto FN nanofibers were imaged with AFM, TEM, and confocal laser scanning microscopy, and the results show that the created FN nanofibers can serve as feasible templates to organize QDs for construction of biophotonic nanohybrids. The PNF–QD nanohybrids have potential applications in optical, biomedical and nanotechnological fields.